From c0f003779d1f54aefbfb7729841c12bcfc930964 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Mon, 14 Dec 2020 13:39:03 -0500
Subject: [PATCH] =?UTF-8?q?=E2=9C=A8=20vernacular=20names?=
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---
 Project.toml            |  2 +-
 docs/src/namefinding.md |  8 ++++++++
 src/NCBITaxonomy.jl     |  3 +++
 src/vernacular.jl       | 15 +++++++++++++++
 test/taxid.jl           |  8 ++++++++
 5 files changed, 35 insertions(+), 1 deletion(-)
 create mode 100644 src/vernacular.jl

diff --git a/Project.toml b/Project.toml
index aeaaf8e..4b54251 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "NCBITaxonomy"
 uuid = "f88b31d2-eb98-4433-b52d-2dd32bc6efce"
 authors = ["Timothée Poisot <timothee.poisot@umontreal.ca>"]
-version = "0.0.5"
+version = "0.0.6"
 
 [deps]
 Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45"
diff --git a/docs/src/namefinding.md b/docs/src/namefinding.md
index bc31e8b..165c553 100644
--- a/docs/src/namefinding.md
+++ b/docs/src/namefinding.md
@@ -4,6 +4,7 @@
 
 ```@docs
 taxid
+vernacular
 ```
 
 The `taxid` function will return a `NCBITaxon` object, which has two fields:
@@ -28,6 +29,13 @@ the *scientific name* will be returned, no matter what you search
 taxid("cow")
 ```
 
+This may be a good point to note that we can use the `vernacular` function to
+get a list of NCBI-known vernacular names:
+
+```@example taxid
+taxid("cow") |> vernacular
+```
+
 You can pass an additional `fuzzy=true` keyword argument to the `taxid` function
 to perform fuzzy name matching using the Levenshtein distance:
 
diff --git a/src/NCBITaxonomy.jl b/src/NCBITaxonomy.jl
index 7e47672..6544374 100644
--- a/src/NCBITaxonomy.jl
+++ b/src/NCBITaxonomy.jl
@@ -43,4 +43,7 @@ export children, descendants
 include("lineage.jl")
 export lineage, parent, rank
 
+include("vernacular.jl")
+export vernacular
+
 end
diff --git a/src/vernacular.jl b/src/vernacular.jl
new file mode 100644
index 0000000..94586a3
--- /dev/null
+++ b/src/vernacular.jl
@@ -0,0 +1,15 @@
+"""
+    vernacular(t::NCBITaxon)
+
+This function will return `nothing` if no vernacular name is known, and an array
+of names if found. It searches the "common name" and "genbank common name"
+category of the NCBI taxonomy name table.
+"""
+function vernacular(t::NCBITaxon)
+    names_from_tax = filter(r -> r.tax_id == t.id, NCBITaxonomy.names_table)
+    common_names = filter(r -> r.class == NCBITaxonomy.class_common_name, names_from_tax)
+    genbank_names = filter(r -> r.class == NCBITaxonomy.class_genbank_common_name, names_from_tax)
+    all_names = vcat(common_names.name, genbank_names.name)
+    length(all_names) == 0 && return nothing
+    return unique(all_names)
+end
\ No newline at end of file
diff --git a/test/taxid.jl b/test/taxid.jl
index bca1749..efc14c3 100644
--- a/test/taxid.jl
+++ b/test/taxid.jl
@@ -38,4 +38,12 @@ module TestTaxid
     chicken = taxid("tchiken"; fuzzy=true, verbose=true)
     @test typeof(chicken) == NCBITaxon
 
+    #Vernacular name
+    chub = vernacular(ncbi"Leuciscus cephalus")
+    @test "European chub" in chub
+    @test "chub" in chub
+    
+    # Vernacular missing
+    @test isnothing(vernacular(ncbi"Lamellodiscus elegans"))
+
 end